Macro
- A list of Jmol / JSmol Tutorials written by users.
- Using the mouse (English · Español · Français · Japanese).
- Scripting quickstart: rendering options · selecting atoms.
- How to create surfaces and isosurfaces, including cavities, pockets and tunnels.
- Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations.
- Creating movies.
- Customizing Jmol: macros · menus.
- Web pages without writing code by using the Jmol "Export to Web" function.
Contents
Introduction to macros in Jmol application
A Jmol macro is a small script that provides some reusable functionality for the Jmol Application. It is saved as a simple text file, like any other script, in the $HOME/.jmol/macros subdirectory. It will show up in the Macro menu of the Jmol application.
Windows: the $HOME folder's location is stored in the environment variable
%USERPROFILE%or in the environment variables%HOMEDRIVE%and%HOMEPATH%; it will usually be atc:\Documents and Settings\(yourUserName)\If you don't find it, try
- My PC > right-click > Properties > Advanced Options (tab) > Environment Variables (button)
- or open a command line and type
set
The macro file must be a text file with the extension macro, and its
contents must be two lines, starting respectively with "Title=" and "Script=" (only one macro per file).
Example macros
(feel free to add your own)
Balls & sticks
To show everything as balls-and-sticks in CPK color, create a text file with this contents:
Title=Ball & Stick Script=select all; color cpk; wireframe only; wireframe 0.15; spacefill 23%;
- (the full script must go in a single line)
and save as ballandstick.macro (or the name you like) in the folder $HOME/.jmol/macros
Then to use it, open Jmol application, open menu "Macros", and there you will have a "Ball & Stick" entry.
Macromolecules, PDB style
To show the protein and nucleic acids as cartoons and the ligands as balls-and-sticks:
Title=PDB view Script=select all; cartoon only; color cartoon chain; select ligand; wireframe 0.15; spacefill 23%; select all;
- (the full script must go in a single line)
Color according to DRuMS MacroMicro scheme
To color the current selection using DRuMS "macromolecule" color scheme (slightly adapted to account for Jmol's capabilities):
Title=color MacroMicro Script=define temp selected; select protein; color [xCBBE8A]; select dna; color [xAE00FE]; select rna; color [xFD0162]; select ligand; color [x6DFA36]; select solvent; color [x3A79BC]; select temp;
- (the full script must go in a single line)
Get current orientation
This would be useful to copy and paste the current orientation of the model into your script.
Title=get orientation Script=show orientation moveTo;
